Skip to main content
. 2020 Dec 22;9:e60987. doi: 10.7554/eLife.60987

Figure 3. Retrotransposons proliferate in HOAP[yak] over experimental evolution.

(A) Replicated experimental evolution strategy that begins with an expanded population of HOAP[mel] and HOAP[yak]. We divided each founder population into three replicates and then froze down 100 females for pool-DNA-seq ('generation 0'). We flipped replicate populations until generation 20, sampling pools of females for DNA-seq at generations 10 and 20 per population. A parallel run of experimental evolution (not shown) was sampled at generations 0, 20, and 50. (B-D) DNA-seq reads mapped to the D. melanogaster HeT-A (B), TAHRE (C), and TART (D) consensus sequences, shown as reads per million (rpm) at a given generation minus the rpm at generation 0 for a given population. The long-term experimental evolution samples have a filled black circle in each square. Note the different y-axes of (B), (C), and (D).

Figure 3—source data 1. Change in read count across original ‘O’ lines and replicated lines (‘A’, ‘B’, ‘C’).
‘Gen’=generation.

Figure 3.

Figure 3—figure supplement 1. Hemizygous cav recapitulates the elevated telomeric retrotransposon copy number of HOAP[yak].

Figure 3—figure supplement 1.

(A) By injecting gRNAs only into Cas9-expressing embryos, we generated a deletion that encompassed the enitre cav coding sequence (light blue rectangle). Below is a browser shot of the BLAT result (https://genome.ucsc.edu/) using the PCR-amplified deleted region as the query. This allele is homozygous lethal (as are cav[deletion] / cav[1] flies). (B) We generated a rescue trangene amplified from a 'wildtype' stock (w[1118]) and, using PhiC31 integrase, inserted the transgene on chromosome II. The transgene rescued viability of otherwise homozygous lethal cav[deletion] flies. (C) Experimental evolution of two replicate populations of the cav[deletion]/TM6b stock results in elevated HeT-A and TART genomic copy number, revealed by sequencing generation 0 and generation 10 populations. Y-axis is reads per million (rpm) at generation 10 minus rpm at generation 0 (with standard error). Circles represent the copy number estimates from the two replicate populations.